The authors describe a fluorometric aptamer based assay for adenosine triphosphate (ATP). It is based on the use of carbon dots (CDs) and graphene oxide (GO). The resultant CD-aptamer is adsorbed on the surface of GO via π-stacking and hydrophobic interaction, and the fluorescence of CD-aptamer is quenched via fluorescence resonance energy transfer (FRET) between CDs and GO. If ATP is present, it will bind to the aptamer and the CD-aptamer will be desorbed from GO. This will suppress FRET and the fluorescence of the CDs is restored. Under the optimal conditions and at typical excitation/emission wavelengths of 358/455 nm, the assay has a 80 pM detection limit and a linear range that extends from 0.10 to 5.0 nM concentrations of ATP. The method was successfully applied to the determination of ATP in yogurt samples. This method can also be conceivably applied to the detection of other analytes for which appropriate aptamers are available.
Graphical abstract Schematic of a novel fluorometric ATP assay based on the fluorescence resonance energy transfer (FRET) between aptamer modified carbon dots (CD-aptamer) and graphene oxide (GO). CD-aptamer was used as the energy donor and molecular recognition probe, and GO acted as energy acceptor. This assay exhibits high sensitivity and selectivity with a detection limit as low as 80 pM.
The authors describe a fluorometric assay for microRNA. It is based on two-step amplification involving (a) strand displacement replication and (b) rolling circle amplification. The strand displacement amplification system is making use of template DNA (containing a sequence that is complementary to microRNA-21) and nicking enzyme sites. After hybridization, the microRNA strand becomes extended by DNA polymerase chain reaction and then cleaved by the nicking enzyme. The DNA thus produced acts as a primer in rolling circle amplification. Then, the DNA probe SYBR Green II is added to bind to ssDNA to generate a fluorescent signal which increases with increasing concentration of microRNA. The method has a wide detection range that covers the10 f. to 0.1 nM microRNA concentration range and has a detection limit as low as 1.0 fM. The method was successfully applied to the determination of microRNA-21 in the serum of healthy and breast cancer patients.
Graphical abstract Schematic of a fluorometric microRNA assay based on two-step amplification involving strand displacement replication and rolling circle amplification. DNA probe SYBR Green II is then bound to ssDNA to generate a fluorescent signal which increases with increasing concentration of microRNA.
The authors describe a fluorometric method for improving the determination of the cancer biomarker 8-hydroxy-2′-deoxyguanosine (8-OHdG). A nicking endonuclease (NEase)-powered 3-D DNA nanomachine was constructed by assembling hundreds of carboxyfluorescein-labeled single strand oligonucleotides (acting as signal reporter) and tens of swing arms (acting as single-foot DNA walkers) on a gold nanoparticle (AuNP). The activity of this DNA nanomachine was controlled by introducing the protecting oligonucleotides. In the presence of aptamer against 8-OHdG, the protecting oligonucleotides are removed from the swing arms by toehold-mediated strand displacement reaction. In the next step, detached DNA walker hybridizes to the labelled DNA so that the DNA nanomachine becomes activated. Special sequences of signal reporter in the formed duplex can be recognized and cleaved by NEase. As a result, the DNA walker autonomously and progressively moves along the surface of the AuNP, thereby releasing hundreds of signal reporters and causing a rapid increase in green fluorescence. This 3-D nanomachine is highly efficient because one aptamer can release hundreds of signal reporters. These unique properties allowed for the construction of a DNA nanomachine-based method for sensitively detecting 8-OHdG in concentrations as low as 4 pM. This is three orders of magnitude lower compared to previously reported methods.
Graphical abstract Schematic of a fluorometric method for determination of the cancer biomarker 8-hydroxy-2′-deoxyguanosine. A nicking endonuclease powered 3D-DNA nanomachine was used to improve the sensitivity. Limit of detection is three orders of magnitude lower than reported methods.
Microcystin-RR (MC-RR) is a highly acute hepatotoxin produced by cyanobacteria. It is harmful to both humans and the environment. A novel aptamer was identified by the systemic evolution of ligands by exponential enrichment (SELEX) method as a recognition element for determination of MC-RR in aquatic products. The graphene oxide (GO) SELEX strategy was adopted to generate aptamers with high affinity and specificity. Of the 50 aptamer candidates tested, sequence RR-33 was found to display high affinity and selectivity, with a dissociation constant of 45.7 ± 6.8 nM. Aptamer RR-33 therefore was used as the recognition element in a fluorometric assay that proceeds as follows: (1) Biotinylated aptamer RR-33 is immobilized on the streptavidinylated wells of a microtiterplate, and carboxyfluorescein (FAM) labelled complementary DNA is then allowed to hybridize. (2) After removal of excess (unbound) cDNA, sample containing MC-RR is added and incubated at 37 °C for 2 h. (3) Displaced free cDNA is washed away and fluorescence intensity measured at excitation/emission wavelengths of 490/515 nm. The calibration plot is linear in the 0.20 to 2.5 ng·mL?1 concentration range, and the limit of detection is 80 pg·mL?1. The results indicate that the GO-SELEX technology is appropriate for the screening of aptamers against small-molecule toxins. The detection scheme was applied to the determination of MC-RR in (spiked) water, mussel and fish and gave recoveries between 91 and 98 %. The method compares favorably to a known ELISA. Conceivably, this kind of assay is applicable to other toxins for which appropriate aptamers are available.
Graphical abstract The aptamer RR-33 specific for microcystin (MC-RR) was identified by using the graphene oxide (GO) SELEX process. This aptamer was used for determination of MC-RR by a fluorometric displacement assay.
A fluorometric aptamer-based assay for ochratoxin A (OTA) is described. It is making use of magnetic separation and a cationic conjugated fluorescent polymer. Amino-tagged aptamer (Apt) against OTA is immobilized on magnetic beads (MBs) to form a conjugate of type Apt-MBs. The immobilized aptamer is partially complementary to carboxyfluorescein-labeled DNA which binds to the Apt-MBs via hybridization if OTA is absent. Only few FAM-DNA will remain in the supernatant after magnetic separation, and only weak fluorescence resonance energy transfer (FRET) occurs on addition of the fluorescent polymer. If, however, OTA is present, it will bind to the aptamer and prevent the hybridization between Apt-DNA and FAM-DNA. This results in the presence of large amounts of FAM-DNA in the supernatant after magnetic separation. On addition of fluorescent polymer, efficient FRET occurs from the polymer to FAM-DNA. Fluorescence, best measured at excitation/emission peaks of 370/530 nm, increases with increasing concentrations of OTA. This assay is highly sensitive and selective. The detection limit is as low as 0.11 ng mL?1. This is 6 times lower than the aptamer assay without using the fluorescent polymer. Conceivably, this method has a wider scope in that it may be extended to other mycotoxins by simply changing the aptamer.
Graphical Abstract Schematic of a fluorometric aptamer assay for ochratoxin A (OTA). It is based on magnetic separation coupled with a cationic conjugated polymer (PFP).
A nanocomposite prepared from reduced graphene oxide (rGO) and silver nanoparticles (AgNPs) is used in an electrochemical aptasensor for the sensitive and selective determination of the antibiotic chloramphenicol (CAP). The nanocomposite was obtained by electrostatic assembly of AgNPs on the surface of polyelectrolyte-functionalized rGO and then used to modify a glassy carbon electrode. The biosensor is then obtained by immobilizing the aptamer against CAP. When incubated with solutions of CAP, the sensor surface is loaded with CAP due to aptamer recognition. The captured CAP can be electrochemically reduced to yield a current that is strongly enhanced as a result of the excellent electrocatalysis property of the graphene/AgNP-nanocomposite. Under optimum conditions, the calibration plot is linear in the 0.01 to 35 μM concentration range, with a 2 nM detection limit (at 3σ). The sensor is reproducible, stable, selective over homologous interferents, and performs excellently when analyzing CAP in milk samples.
Graphical Abstract A graphene/silver nanoparticle-based electrochemical aptasensor is designed for the selective determination of the antibiotic chloramphenicol (CAP). The excellent electrocatalytic reduction of CAP specifically captured onto the electrode surface enables the sensitive electrochemical signal transduction of the biosensor by linear sweep voltammetry (LSV).
The authors describe a method for DNA target recognition and signal amplification that is based on the target-induced formation of a three way junction. The subsequent assembly of two DNA probes releases the inhibitory strand and triggers a downstream strand displacement amplification. This causes the formation of a G-rich single sequence that binds to a hemin monomer with its peroxidase-mimicking properties. The resulting peroxidase (POx) activity is quantified by using H2O2 and TMB as the substrate. In the presence of an inhibitor, in contrast, the POx-like activity is strongly reduced. This forms the basis for a highly sensitive DNA assay. It has a 0.8 pM detection limit when operated at a wavelength of 450 nm and was applied to the isothermal determination of target DNA with high selectivity.
Graphical abstract Schematic of the assay: Introduction of target results in the formation of a three way junction. The subsequent assembly of two probes releases the inhibitory strand and triggers a downstream strand displacement amplification, generating amount of G-rich single sequence which causes peroxidase-mimicking activity on binding to a hemin monomer.
An aptamer based assay is described for the colorimetric detection of adenosine. The presence of adenosine triggers the deformation of hairpin DNA oligonucleotide (HP1) containing adenosine aptamer and then hybridizes another unlabeled hairpin DNA oligonucleotide (HP2). This leads to the formation of a double strand with a blunt 3′ terminal. After exonuclease III (Exo III)-assisted degradation, the guanine-rich strand (GRS) is released from HP2. Hence, the adenosine-HP1 complex is released to the solution where it can hybridize another HP2 and initiate many cycles of the digestion reaction with the assistance of Exo III. This leads to the generation of a large number of GRS strands after multiple cycles. The GRS stabilize the red AuNPs against aggregation in the presence of potassium ions. If, however, GRS forms a G-quadruplex, it loses its ability to protect gold nanoparticles (AuNPs) from salt-induced AuNP aggregation. Therefore, the color of the solution changes from red to blue which can be visually observed. This colorimetric assay has a 0.13 nM detection limit and a wide linear range that extends from 5 nM to 1 μM.
Graphical abstract Schematic presentation of a colorimetric aptamer biosensor for adenosine detection based on DNA cycling amplification and salt-induced aggregation of gold nanoparticles.
An electrochemiluminescent (ECL) aptamer based method is described for the determination of thrombin. Three-dimensional nitrogen-doped graphene oxide (3D-NGO) was placed on a glassy carbon electrode (GCE) to provide an electrode surface that displays excellent electrical conductivity and acts as a strong emitter of ECL. The modified electrode was further coated with chitosan via electrodeposition. Finally, the amino-modified aptamer was immobilized on the modified GCE. The interaction between thrombin and aptamer results in a decrease in ECL. The assay has a linear response in the 1 fM to 1 nM thrombin concentration range and a 0.25 fM lower detection limit (at an S/N ratio of 3). The method was applied to the determination of thrombin in spiked human plasma samples, and recoveries ranged between 94 and 105% (with RSDs of <3.6%). The calibration plot was recorded at potential and wavelength of fluorescence emission (wavelength:?445 nm; potential:?0 to -2 V).
Graphical abstract A bare glassy carbon electrode (GCE) does not display electrochemiluminescence (ECL). If, however, nitrogen-doped graphene quantum dots, chitosan, and three-dimensional nitrogen-doped graphene oxide (NGQD-chitosan/3D-NGO) are electrodeposited on the GCE, strong ECL can be observed. The ECL intensity decreased after aptamer and bovine serum albumin (BSA) were dropped onto the electrode (curve a). However, the ECL further decreases after addition of thrombin (TB; curve b).
A fluorometric patulin (PAT) assay is presented that is based on the use of magnetic reduced graphene oxide (rGO) and DNase I. The fluorescence of the PAT aptamer labelled with 6-carboxyfluorescein (FAM) is quenched by magnetized reduced graphene oxide (rGO-Fe3O4) due to fluorescence resonance energy transfer (FRET). However, in the presence of PAT, the labelled aptamer is stripped off from rGO-Fe3O4. The rGO-Fe3O4 is then magnetically separated so that the fluorescence of free labelled PAT aptamer is restored. DNase I cannot hydrolyze the aptamer on rGO-Fe3O4, but it can cleave the free aptamer-PAT complex. This will release FAM and PAT which can undergo a number of additional cycles to trigger the cleavage of abundant aptamer. Recycling of DNase I-assisted target therefore leads to a strong amplification of fluorescence and consequently to an assay with low limit of detection. The detection limit for PAT is as low as 0.28 μg L?1 which is about 13 times lower than that without using DNase I. The method offers a new approach towards rapid, sensitive and selective detection based on an aptamer. Conceivably, it has a wide scope in that it may be applied to numerous other analytes if appropriate aptamers are available.
Abstract Schematic of a fluorometric assay based on the use of magnetic graphene oxide and DNase I. It was applied to the determination of patulin. DNase I was introduced for recycling amplification. The detection limit is about 13 times lower than that without using DNase I. Figure a contains poor quality of text in image. Otherwise, please provide replacement figure file.Thank you. I will provide the figure file.
A multifunctional fluorescent probe is synthesized for the determination of adenosine 5′-triphosphate (ATP). The 6-carboxyfluorescein-labeled aptamer (FAM-aptamer) was bound to the surface of magnetite nanoparticles coated with polydopamine (Fe3O4@PDA) by π-π stacking interaction to form the multifunctional probe. The probe has three functions including recognition, magnetic separation, and yielding a fluorescent signal. In the presence of ATP, FAM-aptamer on the surface of the probe binds to ATP and returns to the solution. Thus, the fluorescence of the supernatant is enhanced and can be related to the concentration of ATP. Fluorescence intensities were measured at excitation/emission wavelengths of 494/526 nm. Response is linear in the 0.1–100 μM ATP concentration range, and the detection limit is 89 nM. The probe was applied to the quantitation of ATP in spiked human urine and serum samples, with recoveries ranging between 94.8 and 102%.
Graphical abstract A multifunctional fluorescent probe based on the use of FAM-aptamer and Fe3O4@PDA is described for the determination of ATP in spiked human urine and serum samples. FAM-aptamer: 6-carboxyfluorescein-labeled aptamer; Fe3O4@PDA: magnetite nanoparticles coated with polydopamine. ATP: adenosine 5′-triphosphate.
Cobalt oxyhydroxide (CoOOH) nanosheets are efficient fluorescence quenchers due to their specific optical properties and high surface area. The combination of CoOOH nanosheets and carbon dots (CDs) has not been used in any aptasensor based on fluorescence quenching so far. An aptamer based fluorometric assay is introduced that is making use of fluorescent CDs conjugated to the aptamer against methamphetamine (MTA), and of CoOOH nanosheets which reduce the fluorescence of the CDs as a quencher. The results revealed that the conjugated CDs with aptamers were able to enclose the CoOOH nanosheets. Consequently, fluorescence is quenched. If the aptamer on the CD binds MTA, the CDs are detached from CoOOH nanosheets. As a result, fluorescence is restored proportionally to zhe MTA concentration. The fluorometric limit of detection is 1 nM with a dynamic range from 5 to 156 nM. The method was validated by comparing the results obtained by the new method to those obtained by ion mobility spectroscopy. Theoretical studies showed that the distance between CoOOH nanosheet and C-Ds is approximately 7.6 Å which can illustrate the possibility of FRET phenomenon. The interactions of MTA and the aptamer were investigated using molecular dynamic simulation (MDS).
Graphical abstract Carbon dots (C-Ds) were prepared from grape leaves, conjugated to aptamer, and adsorbed on CoOOH nanosheets. So, the fluorescence of C-Ds is quenched. On addition of MTA, fluorescence is restored.
A battery of logic gates, “YES”, “AND” and “OR”, are constructed using magnetic beads (MBs) modified by DNA which consists of a substrate strand (S) and a signal strand on which the logic operates. Inputs stemming from micro-RNA (which represent three cancer biomarkers) take the place of signal DNA. The released signal strand self-assembles into the hemin-G-quadruplex complex (DNAzyme) that catalyzes a blue-green dye (ABTS+) from the precursor ABTS. This dye (quantified at a wavelength of 414 nm) represents the output signal for the various logic gates. The method allows quantitative detection of microRNA of three kinds of logic gates in the range of 5 nM–500 nM with detection limits of 3.8 nM, 4.9 nM, 5.4 nM. Boolean logic circuitry is also achieved following the principles of multilevel strand displacement. Based on strand displacement and magnetic separation, this work demonstrates the possibility of designing a logic system using micro-RNA in live cell lysate as inputs, and its potential application in DNA computation and cancer diagnosis.
Graphical abstract Schematic representation of a battery of logic gates and the Boolean logic circuitry based on strand displacement and magnetic separation responding to multiple microRNA in cancer cell lysate.
The authors describe a fluorometric assay for ochratoxin A (OTA) that is based on the use of graphene oxide and RNase H-aided amplification. On addition of OTA, cAPT is replaced from the APT/cAPT hybridization complex and then hybridizes with RNA labeled with a fluorophore at the 5′-end. Eventually, the fluorophore is released by RNase H cleavage. As the concentration of OTA increases, more cAPTs are displaced, this leading to fluorescence enhancement (best measured at excitation/emission wavelengths of 495/515 nm). This RNase H-assisted cycle response results in strong signal amplification. The limit of detection, calculated on the basis of a signal to noise ratio of 3, is 0.08 ng·mL?1. Response is linear in the 0.08–200 ng·mL?1 OTA concentration range. The method is highly selective for OTA over ochratoxin B and aflatoxin B1. It was applied to the determination of OTA in red wine samples spiked at levels of 1, 7, and 50 ng·mL?1, and the recoveries ranged from 90.9 to 112%.
The authors describe an electrochemical method for the determination of the single-stranded DNA (ssDNA) oligonucleotide with a sequence derived from the genom of hepatitis B virus (HBV). It is making use of circular strand displacement (CSD) and rolling circle amplification (RCA) strategies mediated by a molecular beacon (MB). This ssDNA hybridizes with the loop portion of the MB immobilized on the surface of a gold electrode, while primer DNA also hybridizes with the rest of partial DNA sequences of MB. This triggers the MB-mediated CSD. The RCA is then initiated to produce a long DNA strand with multiple tandem-repeat sequences, and this results in a significant increase of the differential pulse voltammetric response of the electrochemical probe Methylene Blue at a rather low working potential of ?0.24 V (vs. Ag/AgCl). Under optimal experimental conditions, the assay displays an ultrahigh sensitivity (with a 2.6 aM detection limit) and excellent selectivity. Response is linear in the 10 to 700 aM DNA concentration range.
Graphical abstract Schematic of a voltammetric method for the determination of attomolar levels of target DNA. It is based on molecular beacon mediated circular strand displacement and rolling circle amplification strategies. Under optimal experimental conditions, the assay displays an ultrahigh sensitivity with a 2.6 aM detection limit and excellent selectivity.
The authors describe a colorimetric method for the determination of Hg(II) ion. It is based on the color change from red to colorless as displayed by gold nanoparticle (AuNP) modified with thymine - rich DNA. Signal amplification is accomplished by free strand displacement recycling. In this strategy, Hg(II) unfolds the arch-trigger duplex due to the high affinity between Hg(II) and the thymines to form T-Hg(II)-T structures, thereby causing the release of trigger. The liberated trigger unfolds the hairpin structure of H1, and unfolded H1 further unfolds with H2. As a result, the H2 hairpin displaces trigger, and the released trigger unfolds another H1. This results in strong and enzyme-free strand displacement recycling amplification. The aggregation of DNA-AuNPs occurs in the presence of the duplex formed by hairpins H2 and H1. This results in a color change from red to colorless that can be visually observed. Under optimal conditions, the assay has a detection range over 4 orders of magnitude and a 3.4 nM detection limit. The assay is selective, sensitive, rapid and cost-effective. In our perception, it represents a useful platform for determination of Hg(II).
Graphical abstract Schematic presentation of the simple, rapid, low cost colorimetric detection of mercury(II) based on enzyme-free strand displacement amplification along with DNA-labeled AuNP.
This article reviews the progress made in the past 5 years in the field of direct and non-enzymatic electrochemical sensing of glucose. Following a brief discussion of the merits and limitations of enzymatic glucose sensors, we discuss the history of unraveling the mechanism of direct oxidation of glucose and theories of non-enzymatic electrocatalysis. We then review non-enzymatic glucose electrodes based on the use of the metals platinum, gold, nickel, copper, of alloys and bimetals, of carbon materials (including graphene and graphene-based composites), and of metal-metal oxides and layered double hydroxides. This review contains more than 200 refs.
Figure This article reviews the history of unraveling the mechanism of direct electrochemical glucose oxidation and the attempts to successfully develop non-enzymatic electrochemical glucose sensors over the past 5 years.
An electrochemical nanoaptasensor is described that is based on the use of a glassy carbon electrode (GCE) modified with electrodeposited silver nanoparticles (AgNPs). An aptamer (Apt) against trinitrotoluene (TNT) was then immobilized on the AgNPs. The addition of TNT to the modified GCE leads to decrease in peak current (typically measured at a potential of ?0.45 V vs. Ag/AgCl) of riboflavin which acts as an electrochemical probe. Even small changes in the surface (as induced by binding of Apt to TNT) alter the interfacial properties. As a result, the LOD is lowered to 33 aM, and the dynamic range extends from 0.1 fM to 10 μM without sacrificing specificity.
Graphical abstract Schematic presentation of a nanoaptasensor which is based on a glassy carbon electrode (GCE) modified with electrodeposited silver nanoparticles (AgNPs) and aptamer (Apt). It was applied to the detection of 2,4,6-trinitrotoluene (TNT) with the help of riboflavin (RF) as a redox probe.
The authors describe an electrochemical aptamer based assay for the determination of the serine protease lysozyme in very low (pM) concentrations. The method is based on the formation of a complex between anti-lysozyme aptamer fragments and lysozyme, and on electrochemical detection by differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). The surface of a glassy carbon electrode was modified with a nanocomposite consisting of gold nanoparticles and electrochemically reduced graphene oxide nanosheets (AuNPs/erGO), and the thiolated aptamer was then linked to the AuNPs by self-assembly through Au-S bonds. The interaction of immobilized aptamers with lysozyme leads to the decreased peak current in DPV and increased charge transfer resistance (Rct) in EIS when using hexacyanoferrate or Methylene Blue as a redox probe. The calibration plot, when applying EIS and working at a typical voltage of ?0.22 V (vs. SCE), is linear over 1.0 to 104.3 pM concentration range, with a detection limit of 0.06 pM (at a signal-to-noise ratio of 3). The respective data for DPV are a 9.6–205.5 pM linear range with a detection limit of 0.24 pM. Depending on the redox marker applied, the method works in the “signal-off” or “signal-on” mode in DPV and EIS protocols, respectively. The sensing interface is high specific for lysozyme and not affected by other proteins. The method was applied to the determination of lysozyme in spiked diluted human serum, and the results agreed well with data obtained with a standard ELISA.
Graphical abstract The surface of a glassy carbon electrode was modified with a nanocomposite consisting of gold nanoparticles and electrochemically reduced graphene oxide nanosheets (AuNPs/erGO). Then, the thiolated aptamer was linked to the AuNPs by self-assembly through Au-S bonds. The modified electrode was applied to the determination of lysozyme with “signal off” and “signal on” strategies.
A composite consisting of chitosan containing azidomethylferrocene covalently immobilized on sheets of reduced graphene oxide was drop-casted on a polyester support to form a screen-printed working electrode that is shown to enable the determination of nitrite by cyclic voltammetry and chronoamperometry. Both reduction and oxidation of nitrite can be accomplished due to the high electron-transfer rate of this electrode. Under optimal experimental conditions (i.e. an applied potential of 0.7 V vs. Ag/AgCl in pH 7.0 solution), the calibration plot is linear in the 2.5 to 1450 μM concentration range, with an ~0.35 μM limit of detection (at a signal-to-noise ratio of 3). The sensor was successfully applied to the determination of nitrite in spiked mineral water samples, with recoveries ranging between 95 and 101 %.
Graphical abstract We describe the design of ferrocene-functionalized reduced graphene oxide electrode and its electrocatalytic properties towards the determination of nitrite. Compared to a reduced graphene oxide electrode, the sensor exhibits enhanced electrocatalytic activity towards both oxidation and reduction of nitrite.
